GGT5

gamma-glutamyltransferase 5, the group of Gamma-glutamyltransferases

Basic information

Region (hg38): 22:24219654-24245108

Previous symbols: [ "GGTLA1" ]

Links

ENSG00000099998 ∙ NCBI:2687 ∙ OMIM:137168 ∙ HGNC:4260 ∙ Uniprot:P36269 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GGT5 gene.

• not_specified (101 variants)
• not_provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GGT5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004121.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			96	6	1	103
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	96	7	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GGT5	protein_coding	protein_coding	ENST00000398292	12	25489

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.16e-11	0.409	125688	0	59	125747	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.690	315	351	0.896	0.0000215	3661
Missense in Polyphen		123	155.74	0.78978		1672
Synonymous	-1.34	184	162	1.13	0.0000110	1268
Loss of Function	1.16	20	26.5	0.756	0.00000158	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000654	0.000644
Ashkenazi Jewish	0.00	0.00
East Asian	0.000277	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000285	0.000264
Middle Eastern	0.000277	0.000272
South Asian	0.000367	0.000359
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves the gamma-glutamyl peptide bond of glutathione conjugates, but maybe not glutathione itself. Converts leukotriene C4 (LTC4) to leukotriene D4 (LTD4).
• Pathway: Glutathione metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Taurine and hypotaurine metabolism - Homo sapiens (human);Glutathione metabolism;Glutathione conjugation;Metabolism of lipids;Phase II - Conjugation of compounds;Prostaglandin Leukotriene metabolism;Synthesis of Leukotrienes (LT) and Eoxins (EX);Arachidonic acid metabolism;Biological oxidations;Metabolism;Fatty acid metabolism;Glutathione synthesis and recycling;Aflatoxin activation and detoxification (Consensus)

Intolerance Scores

• loftool: 0.822
• rvis_EVS: -0.37
• rvis_percentile_EVS: 28.2

Haploinsufficiency Scores

• pHI: 0.0504
• hipred: N
• hipred_score: 0.199
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.432

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ggt5
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; pigmentation phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype

Gene ontology

• Biological process: translation;proteolysis;cellular amino acid metabolic process;glutamate metabolic process;fatty acid metabolic process;leukotriene metabolic process;glutathione metabolic process;glutathione biosynthetic process;glutathione catabolic process;inflammatory response;cysteine biosynthetic process;leukotriene D4 biosynthetic process
• Cellular component: plasma membrane;integral component of membrane;intrinsic component of plasma membrane
• Molecular function: peptidyltransferase activity;leukotriene-C(4) hydrolase;glutathione hydrolase activity;hypoglycin A gamma-glutamyl transpeptidase activity;leukotriene C4 gamma-glutamyl transferase activity